Hello I have a vcf file like this:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT R4157 R4158 R4163
chr7 30902031 . C A . . PR GT 0/0 0/0 0/0
now I want to convert it to the format like that:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT R4157 R4158 R4163
chrC07 30902031 . C A . . PR GT C C C
So could anyone know to to make it ?Thanks !!!
What does
C
mean for an individual? Shouldn't that be CC for a diploid genome?yeah,
C
meansCC
, and if it isCA
,we useN
orY
to represent itwhy do you want to do this ? what is your final aim ?
Thank you for your reply!Now I get a GWAS result , and I want to analysis some genes if there are any snps located on them.Then I need to know whether these snps will affect the functions of genes!
Hello taoyan,
but than I think it is not a good idea to convert the genotypes in that way. A lot of programs work with the format 0/0 etc. as it is much faster to catch whether you have a reference or in alternative allele.
So please check first what the expected input for the programs you like to use is.
fin swimmer